Variant report

Variant	rs12936539
Chromosome Location	chr17:33938696-33938697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:33933853..33936154-chr17:33937625..33939956,2	K562	blood:
2	chr17:33933800..33936366-chr17:33936981..33942006,8	K562	blood:
3	chr17:33913439..33918333-chr17:33935583..33940121,6	K562	blood:
4	chr17:33929073..33932041-chr17:33938211..33940599,2	K562	blood:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11650225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650621	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651380	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652390	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653354	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654542	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656872	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11657558	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936693	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939138	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12939481	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940422	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940584	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12943224	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945102	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945980	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947274	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12951703	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17606150	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17608253	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638076	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669281	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670584	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17670614	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17676508	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34063751	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34874930	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34937989	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3506	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515868	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672532	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774966	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531775	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71381460	1.00[ASN][1000 genomes]
rs71381461	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381463	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71381464	0.83[AFR][1000 genomes]
rs71381465	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381467	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71381469	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
2	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
3	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:33916800-33945400	Weak transcription	Stomach Mucosa	stomach
5	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:33919400-33940000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:33920600-33939800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr17:33920600-33939800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr17:33920600-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:33920600-33940000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr17:33920600-33940200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr17:33920600-33942200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:33920600-33942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:33920600-33944000	Strong transcription	Dnd41	blood
15	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:33921000-33939800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:33921000-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:33921000-33940400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:33921000-33941400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:33921000-33942200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr17:33921000-33943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:33921000-33946200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:33921000-33946600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:33921200-33939600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr17:33921200-33939800	Strong transcription	Primary T cells from cord blood	blood
28	chr17:33921200-33939800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr17:33921200-33940000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:33921200-33940000	Strong transcription	Adipose Nuclei	Adipose
31	chr17:33921600-33939400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:33921800-33939800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr17:33921800-33939800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr17:33921800-33944000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:33922000-33938800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:33923800-33940600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:33924600-33939800	Strong transcription	Liver	Liver
38	chr17:33924600-33941400	Weak transcription	Psoas Muscle	Psoas
39	chr17:33926000-33955200	Weak transcription	Pancreas	Pancrea
40	chr17:33926200-33943800	Weak transcription	Fetal Heart	heart
41	chr17:33926800-33952600	Weak transcription	Fetal Brain Male	brain
42	chr17:33929800-33942200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr17:33930600-33938800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:33930800-33939000	Strong transcription	Fetal Intestine Small	intestine
45	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:33931800-33942400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:33932400-33939200	Strong transcription	Fetal Thymus	thymus
48	chr17:33932400-33940000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr17:33932400-33942200	Strong transcription	Fetal Muscle Leg	muscle
50	chr17:33932600-33940000	Strong transcription	HUVEC	blood vessel

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